Contacts of the helix formed by residues 8 - 21 (chain G) in PDB entry 5DPW
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 8 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7G LYS* 1.3 76.5 - - - +
9G LEU* 1.3 66.8 + - - +
10G ALA* 3.3 7.0 + - - +
11G ILE* 3.2 29.1 + - - +
12G ARG* 3.0 29.4 + - - +
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Residues in contact with LEU 9 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8G SER* 1.3 73.3 - - - +
10G ALA* 1.3 57.9 + - - +
12G ARG* 3.3 23.5 + - - +
13G GLN* 2.8 56.3 + - - +
101G GLU* 3.8 30.7 - - + +
102G ASP* 3.5 39.9 - - + +
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Residues in contact with ALA 10 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8G SER* 3.1 10.0 - - - +
9G LEU* 1.3 78.0 - - - +
11G ILE* 1.3 65.4 + - + +
13G GLN* 3.1 17.2 + - - +
14G GLU* 2.8 35.4 + - + +
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Residues in contact with ILE 11 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G LYS* 3.6 47.1 - - + +
8G SER* 3.2 23.6 + - - +
10G ALA* 1.3 87.5 - - + +
12G ARG* 1.3 58.5 + - - +
14G GLU* 3.1 26.9 + - - +
15G GLU* 2.8 41.2 + - + +
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Residues in contact with ARG 12 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3G PHE* 3.7 26.2 - - + -
4G LYS* 3.4 49.7 + - - +
7G LYS* 3.7 19.0 + - + -
8G SER* 3.0 18.0 + - - +
9G LEU* 3.4 36.4 - - - +
11G ILE* 1.3 76.0 - - - +
13G GLN* 1.3 57.4 + - - +
15G GLU* 3.3 9.3 + - - +
16G VAL* 2.9 34.1 + - - +
102G ASP* 3.3 41.9 + - + +
104G PHE* 3.7 3.3 - - + -
106G TYR* 3.3 19.3 - - - -
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Residues in contact with GLN 13 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G LEU* 2.8 50.6 + - + +
10G ALA* 3.3 16.7 - - - +
12G ARG* 1.3 73.9 - - - +
14G GLU* 1.3 59.3 + - - +
16G VAL* 3.9 0.8 - - - +
17G ALA* 2.8 35.7 + - - +
101G GLU 4.1 9.2 + - - +
102G ASP* 3.6 19.7 - - - +
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Residues in contact with GLU 14 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G ALA* 2.8 24.0 + - + +
11G ILE* 3.1 33.2 + - + +
13G GLN* 1.3 72.1 - - - +
15G GLU* 1.3 53.0 + - + +
17G ALA* 3.8 3.4 - - - +
18G GLY* 2.7 32.9 + - - -
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Residues in contact with GLU 15 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3G PHE* 3.7 14.6 - - - -
7G LYS* 4.7 9.5 - - - +
11G ILE* 2.8 35.7 + - + +
12G ARG* 3.5 9.9 - - - +
13G GLN 3.2 0.2 - - - -
14G GLU* 1.3 71.6 - - + +
16G VAL* 1.3 54.8 + - - +
18G GLY* 3.1 2.1 + - - -
19G ILE* 2.8 38.9 + - - +
47G LYS* 3.0 39.0 + - - +
104G PHE* 3.8 7.9 - - + -
4H ASP* 4.7 6.4 - - - +
6H TRP* 4.6 7.8 + - + +
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Residues in contact with VAL 16 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G ARG 2.9 17.2 + - - +
13G GLN* 3.9 1.8 - - - +
15G GLU* 1.3 70.2 - - - +
17G ALA* 1.3 60.8 - - - +
19G ILE* 3.1 10.3 - - - +
20G ARG* 2.9 50.5 + - + +
28G PRO* 4.4 5.6 - - + -
95G TYR* 4.6 2.2 - - - +
102G ASP 3.4 15.0 - - - +
103G GLY* 3.7 27.6 - - - +
104G PHE* 3.2 39.9 - - + -
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Residues in contact with ALA 17 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G GLN 2.8 22.7 + - - +
14G GLU* 4.0 3.6 - - - +
16G VAL* 1.3 74.3 - - - +
18G GLY* 1.3 61.0 + - - +
20G ARG* 4.3 4.3 - - - +
21G ALA* 3.4 24.3 + - - +
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Residues in contact with GLY 18 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G GLU 2.7 23.7 + - - -
15G GLU* 3.4 1.8 - - - -
17G ALA* 1.3 76.6 - - - +
19G ILE* 1.3 60.0 + - - +
21G ALA* 3.6 12.2 + - - +
22G LYS* 4.0 7.1 + - - +
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Residues in contact with ILE 19 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G GLU 2.8 18.6 + - - +
16G VAL* 3.1 15.3 - - - +
18G GLY* 1.3 69.2 - - - +
20G ARG* 1.3 67.9 + - + +
21G ALA 3.0 4.7 - - - -
22G LYS* 2.8 24.7 + - + -
23G PHE* 3.0 25.7 + - + +
28G PRO* 4.9 2.0 - - + -
49G LEU* 3.4 41.3 - - + -
6H TRP* 3.7 41.7 - - + +
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Residues in contact with ARG 20 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16G VAL* 2.9 29.4 + - + +
17G ALA* 4.6 3.8 - - - +
19G ILE* 1.3 81.9 - - + +
21G ALA* 1.3 56.1 + - - +
22G LYS 3.2 1.6 - - - -
23G PHE 3.9 8.9 + - - -
24G PRO* 2.4 59.8 + - - +
25G ASN 4.3 1.0 - - - -
26G LYS 3.3 29.6 + - - +
27G ILE* 4.9 5.2 - - - +
28G PRO* 4.2 9.9 - - + -
49G LEU* 5.9 1.1 - - + -
52G GLN* 4.9 5.1 - - - -
95G TYR* 3.4 41.7 + - - -
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Residues in contact with ALA 21 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17G ALA 3.4 18.8 + - - +
18G GLY* 3.8 7.9 - - - +
19G ILE 3.0 1.4 - - - -
20G ARG* 1.3 77.4 - - - +
22G LYS* 1.3 59.7 + - - +
24G PRO* 5.2 2.2 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il